Re: [Spglib-users] Partial site occupancy supported?

[Keith R. <kr...@gm...>]

Dear Togo,

This branch certainly works for my test case.  Given the widespread 
occurrence of site disorder in the ICSD, this capability to analyse 
systems with mixed sites will surely find many uses.

Keith Refson

On 29/10/16 02:30, Atsushi Togo wrote:
> Hi Keith,
>
> You are correct.
>
> 'cel_any_overlap_with_same_type' itself allows to distinguish atomic
> types, but not for many other general routines, i.e., I didn't
> consider something like partial occupancy.
>
> I felt that the change required to make it is not a lot. So I worked
> for it. I first made the function below in cell.c.
>
> int cel_is_overlap_with_same_type(const double a[3],
>  const double b[3],
>  const int type_a,
>  const int type_b,
>  SPGCONST double lattice[3][3],
>  const double symprec);
>
> and replaced the calls of the function 'cel_is_overlap' by this
> function in case required. This modification is pushed to the
> 'overlap_atoms' branch on github. If you are interested in it, you can
> pull it and try.
>
> This change didn't induce any failure of the tests, so I will consider
> this change to be merged to the main branch.
>
> Togo
>
> On Fri, Oct 28, 2016 at 9:07 PM, Keith Refson <kr...@gm...> wrote:
>> Dear list,
>>
>> I read the contents of the changelog for 1.9.5
>>
>>         To check overlap of atoms, 'cel_any_overlap' and
>>         'cel_any_overlap_with_same_type' were implemented. The former
>>         doesn't check atomic type but the later does. Currently this check
>>         is done before symmetry search and the later is used for
>>         it. Therefore overlap of different types of atoms is allowed.
>>
>> to mean that analysis of a cell containing mixed sites with partial
>> occupancy is supported.  But my test - attached - fails in
>> "ssm_get_exact_positions"  as this fails to allow for multiple atoms on the
>> same site.  Specifically the test at line 108 in cite_symmetry.c detects a
>> mismatch.
>>
>> Have I misunderstood the intention, or is this a bug?
>>
>> Keith Refson
>>
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>
>
>